Contacts of the helix formed by residues 180 - 191 (chain Y) in PDB entry 6CP3
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ILE 180 (chain Y).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66 LEU* 5.0 2.7 - - + -
106 GLU* 6.1 0.7 - - - -
164Y LYS* 4.3 17.7 - - + +
165Y GLY 4.0 2.1 + - - -
179Y SER* 1.3 78.1 - - - +
181Y SER* 1.3 67.6 + - - +
182Y THR 3.3 1.8 - - - -
183Y LYS* 2.9 6.2 + - - +
184Y ILE* 2.8 33.9 + - + +
184Z LEU* 6.1 2.5 - - + -
192Z LYS* 3.0 31.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 181 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162Y GLU 5.2 1.8 - - - -
163Y ILE* 3.3 26.5 - - - +
164Y LYS* 3.8 28.5 - - - +
179Y SER* 3.5 1.3 + - - -
180Y ILE* 1.3 78.0 - - - +
182Y THR* 1.3 76.0 + - - +
184Y ILE* 3.2 9.2 + - - +
185Y GLN* 2.9 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 182 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B SER* 5.2 10.1 - - - +
91B LYS* 5.9 4.9 - - - +
163Y ILE* 5.6 0.7 - - + -
177Y ASP* 2.7 44.9 + - - +
179Y SER* 3.9 2.9 + - - -
181Y SER* 1.3 84.4 + - - +
183Y LYS* 1.3 70.2 + - - +
185Y GLN* 3.1 10.4 + - - +
186Y LYS* 2.9 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 183 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46 GLN* 4.6 9.9 + - - +
66 LEU* 3.3 32.4 - - + +
76 TYR* 5.2 5.3 - - - +
106 GLU* 4.3 8.4 + - - +
15B GLU* 4.6 7.6 + - - -
18B ILE* 3.8 30.5 - - + +
19B LYS* 5.3 6.0 - - - +
22B SER* 5.3 11.7 - - - -
177Y ASP 5.6 2.9 - - - +
178Y LEU* 4.7 5.6 - - - +
179Y SER 3.4 19.5 - - - +
180Y ILE* 2.9 9.2 + - - +
182Y THR* 1.3 84.7 + - - +
184Y ILE* 1.3 61.8 + - - +
186Y LYS* 3.2 4.9 + - + +
187Y LEU* 2.6 43.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 184 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106 GLU* 5.5 4.7 - - - +
164Y LYS* 5.2 5.2 - - + -
180Y ILE* 2.8 24.8 + - + +
181Y SER* 3.5 10.3 - - - +
183Y LYS* 1.3 74.8 - - - +
185Y GLN* 1.3 66.1 + - - +
187Y LEU* 3.2 11.1 + - + +
188Y ASN* 2.9 40.4 + - - +
180Z VAL* 4.6 20.2 - - + -
183Z GLU* 6.3 3.1 - - + -
184Z LEU* 4.3 30.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 185 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B SER 4.5 11.3 - - - +
59B SER* 4.2 24.6 + - - -
60B GLY* 4.8 5.5 - - - +
181Y SER 2.9 13.5 + - - +
182Y THR* 3.1 13.9 + - - +
184Y ILE* 1.3 79.1 - - - +
186Y LYS* 1.3 60.1 + - - +
188Y ASN* 3.2 7.6 + - - +
189Y LYS* 2.9 34.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 186 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B ILE* 3.7 35.2 - - + -
182Y THR 2.9 14.7 + - - +
183Y LYS* 3.9 7.2 - - + +
185Y GLN* 1.3 77.8 - - + +
187Y LEU* 1.3 63.7 + - - +
189Y LYS* 3.4 5.2 + - - +
190Y VAL* 3.1 30.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 187 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106 GLU* 3.9 40.2 - - + +
116 LEU* 4.6 7.6 - - + -
146 THR* 5.2 6.7 - - + +
15B GLU* 3.2 42.3 + - + +
183Y LYS* 2.6 41.9 + - + +
184Y ILE* 3.6 9.9 - - + +
186Y LYS* 1.3 77.3 - - - +
188Y ASN* 1.3 65.8 + - - +
190Y VAL* 3.5 2.8 + - - +
191Y LEU* 3.2 24.9 + - - +
176Z VAL* 5.9 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 188 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184Y ILE* 2.9 30.7 + - - +
185Y GLN* 3.4 11.4 - - - +
187Y LEU* 1.3 78.6 - - - +
189Y LYS* 1.3 64.4 + - - +
191Y LEU* 2.9 6.2 + - - -
192Y GLU* 2.9 45.1 + - - +
176Z VAL* 3.5 27.9 - - - +
177Z ILE* 5.4 7.2 - - - +
180Z VAL* 4.6 8.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 189 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185Y GLN* 2.9 24.0 + - + +
186Y LYS* 3.4 7.6 + - - +
188Y ASN* 1.3 76.5 - - - +
190Y VAL* 1.3 63.4 + - + +
191Y LEU 3.4 0.2 + - - -
192Y GLU* 3.5 17.0 + - - +
193Y ASP* 4.4 3.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 190 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B SER* 3.6 24.9 - - - +
14B LEU* 3.6 38.4 - - + -
15B GLU* 4.8 4.0 - - - +
18B ILE* 3.7 22.9 - - + -
186Y LYS 3.1 18.2 + - - +
187Y LEU 4.0 3.6 - - - +
189Y LYS* 1.3 78.2 - - + +
191Y LEU* 1.3 57.6 + - - +
192Y GLU 3.4 1.2 + - - -
193Y ASP* 4.5 10.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 191 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B SER* 5.1 11.9 - - - +
187Y LEU 3.2 16.6 + - - +
188Y ASN* 2.9 8.0 + - - +
190Y VAL* 1.3 76.4 - - - +
192Y GLU* 1.3 63.9 + - - +
193Y ASP 3.4 4.3 - - - -
169Z GLN* 3.4 14.9 + - - -
173Z ALA* 4.8 6.4 - - - +
176Z VAL* 4.5 21.2 - - + +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il